GTN Training: Galaxy 101 For Everyone

introduction-galaxy-reproduce/main-workflow

Author(s)

Version
1
Last updated
Aug 25, 2021
License
None Specified, defaults to CC-BY-4.0
Tags
introduction

Features
Tutorial
How to reproduce published Galaxy analyses
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00115
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on (Dev) WorkflowHub
Launch in Tutorial Mode
Download 
flowchart TD
  0["ℹ️ Input Dataset\niris"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["Convert CSV to tabular"];
  0 -->|output| 1;
  2["Datamash"];
  1 -->|tabular| 2;
  5cfaaba2-39a6-479b-8b4c-7fb1a3c2736e["Output\ndatamash_output"];
  2 --> 5cfaaba2-39a6-479b-8b4c-7fb1a3c2736e;
  style 5cfaaba2-39a6-479b-8b4c-7fb1a3c2736e stroke:#2c3143,stroke-width:4px;
  3["Remove beginning"];
  1 -->|tabular| 3;
  4["Cut"];
  3 -->|out_file1| 4;
  5["Group"];
  3 -->|out_file1| 5;
  25ac263e-3d37-43c9-b8ee-5bf1a7360fe9["Output\ngroup1"];
  5 --> 25ac263e-3d37-43c9-b8ee-5bf1a7360fe9;
  style 25ac263e-3d37-43c9-b8ee-5bf1a7360fe9 stroke:#2c3143,stroke-width:4px;
  6["Group"];
  3 -->|out_file1| 6;
  f1890571-0298-43fa-bdf7-fbaa2d2fc12b["Output\ngroup2"];
  6 --> f1890571-0298-43fa-bdf7-fbaa2d2fc12b;
  style f1890571-0298-43fa-bdf7-fbaa2d2fc12b stroke:#2c3143,stroke-width:4px;
  7["Scatterplot w ggplot2"];
  3 -->|out_file1| 7;
  8["Scatterplot w ggplot2"];
  3 -->|out_file1| 8;
  9["Unique"];
  4 -->|out_file1| 9;
  ec39c0ad-eb26-47d6-b9a7-c2e5ffa043c6["Output\nunique_output"];
  9 --> ec39c0ad-eb26-47d6-b9a7-c2e5ffa043c6;
  style ec39c0ad-eb26-47d6-b9a7-c2e5ffa043c6 stroke:#2c3143,stroke-width:4px;

Inputs

Input Label
iris iris

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0 Datamash
Grouping1 Group
Grouping1 Group
toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/2.2.1+galaxy1 Scatterplot w ggplot2
toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/2.2.1+galaxy1 Scatterplot w ggplot2
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0 Unique

Tools

Tool Links
Cut1
Grouping1
Remove beginning1
csv_to_tabular
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/2.2.1+galaxy1 View in ToolShed

To use these workflows in Galaxy you can either click the links to download the workflows, or you can right-click and copy the link to the workflow which can be used in the Galaxy form to import workflows.

Importing into Galaxy

Below are the instructions for importing these workflows directly into your Galaxy server of choice to start using them!
Hands On: Importing a workflow
  1. Click on Workflows in the Galaxy activity bar (on the left side of the screen, or in the top menu bar of older Galaxy instances). You will see a list of all your workflows
  2. Click on Import at the top-right of the screen
  3. Provide your workflow
    • Option 1: Paste the URL of the workflow into the box labelled “Archived Workflow URL”
    • Option 2: Upload the workflow file in the box labelled “Archived Workflow File”
  4. Click the Import workflow button

Below is a short video demonstrating how to import a workflow from GitHub using this procedure:

Video: Importing a workflow from URL

Version History

Version Commit Time Comments
1 03bdb9f97 2021-07-10 16:43:54 Adding new GTN how to reproduce Galaxy analyses

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-reproduce/workflows/main_workflow.ga -O workflow.ga
workflow-to-tools -w workflow.ga -o tools.yaml
shed-tools install -g GALAXY -a API_KEY -t tools.yaml
workflow-install -g GALAXY -a API_KEY -w workflow.ga --publish-workflows